The parasitic lifestyle of an archaeal symbiont

Abstract

DPANN Archaea are a diverse group typically characterised by small cells and reduced genomes. To date, all cultivated DPANN Archaea are ectosymbionts that require direct cell contact with a host archaeal species for proliferation. However, the dynamics of DPANN – host interactions and the impacts of these interactions on host species are poorly understood. Here, we show that one DPANN archaeon (Candidatus Nanohaloarchaeum antarcticus) engages in parasitic interactions with its host (Halorubrum lacusprofundi) that result in host cell lysis. Our data also suggest that these interactions involve invasion of the host cell by the nanohaloarchaeon. This is the first reported instance of such a predatory-like lifestyle amongst Archaea and indicates that some DPANN Archaea may interact with host populations in a manner similar to viruses.

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Repository contents

1_Phylogenies.tar.gz includes all files needed to generate the phylogeny shown in Figure 4 of the associated manuscript. Specifically, this includes: 

1. The Workflow used to generated the species tree
2. Any required dependencies such as custom scripts or custom databases
3. The protein files from 
   1. The proteins from all archaeal reference genomes that were used to generate the protein tree
   2. The 51 marker proteins used to generate the species tree
4. The mafft_linsi alignments of the 51 marker proteins
5. The BMGE trimmed alignments of the 51 marker proteins
6. The concatenated alignment used to generate the species tree
7. The output of the IQ-TREE analysis

2_Protein_search.tar.gz includes all files needed to generate (a) the HMM profiles specific the two proteins with a coiled-coil protein (CCP) domain (referred to as Locus1 and Locus2 throughout the description) and (b) the Phyre2 results for all potential Locus1 and Locus2 proteins found in the archaea reference set. Specifically, this includes:

(a)

1.  The script used to build the HMM profiles
2. Any required dependencies
3. The sequences of Locus1 and Locus2 proteins, including the individual proteins, the aligned proteins and the trimmed alignments.
4. All HHsearch results
5. The HMM profiles

(b)

1. The results for the batch search run for all potential Locus 1 and Locus2 proteins found across DPANN archaea
2. The results for the sensitive search run for the Locus1 and Locus2 proteins from Cand. N. antarcticus

3_Orthogroup_Data.tar.gz includes all files relating to groups of orthologous proteins generated by OrthoFinder. Specifically this includes:

1. List of assemblies included in the analysis
2. List of the number of proteins belonging to each orthogroup for each genome in the analysis.
3. List of each orthogroup and the identifiers for each protein in each genome that were assigned to that orthogroup.
4. List of the protein IDs for every protein in each orthogroup. Does not contain genome information.
5. List of how many orthogroups are shared between each genome
6. List of genes from each genome not assigned to an orthogroup
7. Distribution of orthogroups across major phyla.
8. General statistics for the orthogroups
9. General statistic for each genome

4_Pili_Phylogenies.tar.gz includes all files relating to generating single genes trees for pili-related genes (archaea-only and archaea and bacterial single protein trees). Includes:

1. A list of investigated Pili genes
2. Separately, for the archaeal-only and archaeal + bacterial species trees the: raw protein files, alignments, trimmed alignments, tree files